I'm confused about how an assimilated individual can 'infect' the collective

The borg assimilate billions of individuals and it doesn't affect them, so I don't see why Hugh would affect them at all. If it were the case that an assimilated drone regains individuality and rejoins the collective, that could cause problems, well this has happened in VOY: survival instinct: the borg just wiped there memory and suppressed the individuality again (no problem). This scenario must have happened enough with stranded drones (VOY can't be the only time in borg history)

So that leaves a huge question, why did Hugh's individuality affect the Collective at all?

It didn't. At most it resulted in a few of his shipmates going a bit wiggins temporatily.
– ValorumOct 7 '16 at 14:57

In Star Trek Online Hugh founded a group of liberated Borg called The Cooperative. STO is pretty much the closest thing we've got to canon post-Nemesis. So it really depends on whether you count it, because AFAIK there's no canon information on whether it affected the Borg. My impression about the episode was that Picard chose to take the chance of giving him individuality over using him as a carrier for a computer virus.
– PointlessSpikeOct 7 '16 at 15:05

agreed but he didn't just say 'hey, I had a great time who's with me', and the Borg are experts in suppressing individuality, I cant understand how his individuality could have had any effect (by collective I did mean the collective on the ship)
– MattOct 7 '16 at 15:29

@Matt What do you mean by "it doesn't affect them"? What is "it"?
– miltonautOct 8 '16 at 0:08

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@miltonaut I mean that they usually just suppress the individuality and use there knowledge with no problems (any other time)
– MattOct 8 '16 at 11:14

1 Answer
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The principle seems to be that when the Collective assimilates an individual, their individuality (along with their other memories) are uploaded into the hive-mind. This mental upload is then processed and any pertinent information is disseminated to all drones everywhere.

Since an individual's feelings of individuality would be neither be pertinent or novel this would obviously be discarded along with any other emotional baggage. This strongly suggest that there's some sort of sandbox area where newly assimilated information can be looked at and cross-compared to all the other things the Collective knows. This prevents individuality from infecting the hive.

BORG QUEEN:You cling to sarcasm because you are afraid to see the truth. Species one zero zero two six is already adding to our perfection. You can feel their distinctiveness coursing through us, enhancing us. Stop resisting. Take pleasure in this.

When a set of rogue drones are found by the Collective (like those seen in Voy: Survival Instinct), they would undoubtedly be treated as highly suspect and be assimilated in almost exactly the same way that a non-Borg would be. The difference here is that because there was no suspicion that Hugh had become an individual, he was accepted back directly into the hive and immediately reintegrated. His memories were uploaded without being sandboxed, firstly into the cube's memory.

What then happened is that this process resulted in a corruption of the Local Collective. When the Greater Collective sensed that there was a problem, they disconnected Hugh's cube from the hive mind entirely. Under normal circumstances this would result in the cube self-destructing, as we saw at the end of 'The Best of Both Worlds, Part 2', dealing with the problem. Apparently the contagion had already spread too far and the ship was simply set adrift.